Genome-wide landscapes of genes and repeatome reveal the genomic differences between the two subspecies of peanut (Arachis hypogaea)

Distribution and structural features of genes, repeat elements and transposable elements (TEs) were studied to identify the genomic differences between the two subspecies (ssp. hypogaea and ssp. fastigiata) of peanut (Arachis hypogaea L.). A total of 67128 predicted genes, 2738666 copies of TEs and 162361 tandem repeats from the reference genome of Tifrunner were employed for this study. Of the 67128 genes, 33622 were reading on the plus strand, while 33506 were traced on the minus strand. Though B03 had the highest number of genes (4524), A08 recorded the highest density (53 genes/Mb) of genes in the genome. Telomeric regions had the highest density of genes. The average length of the genes was 3971 bp with majority of the genes (39228) containing one to five exons. The gene Arahy.11.0DU9MH had the insertion of 28 different types of TEs, and was the longest gene in the peanut genome. A total of 15731 genes were monomorphic in terms of SNPs across 179 accessions, while 7401 genes showed polymorphism at one nucleotide, indicating very low allelic variation at these genes. Remaining 66% of the genes had two or more SNPs, and therefore showed relatively high allelic variation. Among the 101 unique types of TEs, the Retro elements (869279) followed by CACTA (272596) and Mu (250248) TEs were most predominant. Telomeric regions showed less density of TEs than the regions. On an average, each gene contained 1.8 copies of TEs, and 35706 genes did not have the insertion of any TEs. A QTL-Seq approach could identify 186 SNPs and 26 gene differences between the two subspecies of A. hypogaea. Two of the 26 genes showed allelic variation in terms of SNPs and TEs.